When you upload a new version with butler, it only uploads a “patch” which, to put it simply, contains only the changes based on the old version.
The same thing happens on the Itch app, when it updates a game, it only downloads the “patch”, to save space.
I’m not sure if deleting the old file, and uploading a new one with the same “Channel Name” caused some sort of confusion? Especially since you mentioned you encountered the same issue yourself, but it was fixed once you uninstalled and installed again the game.
If that’s what’s happening, I can’t help much more. I would suggest maybe to delete the file, and upload the same build with a new “Channel Name”, but it’s up to you. I can’t guarantee this is the issue you are seeing. Alternatively an admin/mod might see this and provide more details/help.
Also keep in mind the “–useversion” flag does not have any restrictions by default. As in, you can name multiple builds with random numbers as the version number, and butler will still be able to tell which one is new and which one is old. I think there’s a setting on the “Edit Game” page to change that though.